Return Of The Phoenix: Beginnings
by Dagana
Summary: A Little Girl who had been prophesised… A City with a hidden past… The Return Of An Ancient Race… A Family who will battle the odds in the hope of normalcy… The Fight Begins…
1. Chapter 1

**Title**: Return Of The Phoenix: Beginnings

**Series**: Atlantis: The New Order

**Summary**: A Little Girl who had been prophesised… A City with a hidden past… The Return Of An Ancient Race… A Family who will battle the odds in the hope of normalcy… The Fight Begins…

**Genre(s): **Action/Adventure; Hurt/Comfort; Future Fic; Angst; Drama;

**Warnings: **Violence; Character Death;

**Disclaimer:** SGA is not mine, and neither are Sheppard, Weir or the rest of the team. I do own any original characters though, and i'm only playing in Robert Cooper and Brad Wright's Sandbox. So this is all for fun :)

--

**Author's Note:** Okay, this is a re-post of this story, after suffering _MAJOR_ writer's block and losing the chapters i've already written, i've just found them and so i'm going to slowly post the chapters i have and hopefully, i can get some more of the story done- i hand wrote up to chapter ten but i've changed my idea slightly for the plot and so i'm going wherever the story may take me. This was written pre- season three so i'm going with that, so sorry if your looking for Sam Carter as the Atlantis Team Leader- and look out for an old nemesis coming back seemingly from the dead much later in the story...

**--**

**Chapter One: Punishment**

--

"Elizabeth, your pregnant."

Carson Beckett's word's echoed in Elizabeth's mind as she watched John Sheppard's dirt covered shirt being ripped off of him as he was held tightly by the arms as the two men holding him thrust his arms up into shackles above his head as he involuntarily yelped as his right shoulder was dislocated as the guard pulled his arm- John making a futile attempt to resist- A large man came up behind him, holding a cat-o-nine tails, patting the faded whip which had small metal balls on the end of each piece of leather.

Elizabeth's punishment was to watch him suffer because of their failed attempt to escape the prison planet- The two Atlantean leaders had been taken from a mission almost three weeks ago and just a few days before John had put his escape plan into action; They had almost made it to the gate. Almost- when they had been caught. They had been put in a prison cell after giving John a beating when he tried to fight back at the gate but now it was time for both of their punishments.

As Elizabeth was held firmly, a tall dark haired woman dressed solely in Black came to watch. Her name was Beta; An Avatar of immense power, Beta had been known to use her powers to torture a person by using their worst fears against them. Elizabeth watched as she calmly strode around the wooden structure that John was bound to- still standing- before coming to stand in front of him, her back to the crowd as she wrenched John's head back by his dirt covered hair and whispered something in his ear before roughly releasing him and turning back to the crowd who encircled the area.

"This is the punishment for all those who attempt escape and fail- Now this human man who has been so resilient to our preventions will pay the price for both he and his fellow escapee, whose punishment is to watch the man she loves suffer for both of their foolishness… let us see how much fight he has left once his punishment has been given."

The crowd murmured as Beta left the crowded arena- even though Elizabeth knew she would probably be watching- as John and one of the guards standing near him challenged each other as Elizabeth felt hot tears on her cheeks as they escaped involuntarily as the larger man raised the whip high before bringing it down on John's back which caught John unawares as he let out a yell in pain; His legs giving away beneath him at the shock of the metal balls ripping into his flesh.

The large man took his time delivering the blows knowing that it would prolong the prisoners pain.

As John tried to catch his breath, he stole a quick glance at Elizabeth, whose pale face was becoming more tear stained every moment. His face and torso were covered in a thin layer of sweat as his back felt increasingly wet as blood ran down through his pants and to the dirt. As John fought his pain, he gave Elizabeth- who was in the front row of the crowd- a weak attempt at a smile. As his glazed Blue-Grey eyes made contact with her hazel coloured, he silently told her "I love you," As he mouthed those words, the large man lifted the whip over his head. Johnwas unprepared for the blow which caused him to yell once more as the lashed criss crossed his back as more blood seeped from the now deep lashes left by the blood stained metal balls and staind leather of the whips.

"I love you, too," Elizabeth whispered as more blows caused John to grunt in pain- mostly on his back but at least one slashed his front which caused the soldier so much pain that he passed out as his right shoulder began to bleed as one slash went so deep as to reveal his collar bone.

**--**

It was early evening by the time the punishment was completed. After a while of the feared cat-o-nine tails, the whip had been switched with and ordinary one used on animals but John remained in a pattern of passing out after every few blows and had to be startled awake by buckets of ice-cold water being splashed over him.

When his arms were released from the shackles, John collapsed in a heap in the dirt as Elizabeth rushed over to him and turned the injured man over which caused John to whimper as she placed his head on her lap as she cried openly as the crowd dissolved until there was only a trickle of people, mostly guards, and kissed his forehead reverently as John lay with his right arm across his stomach as he whimpered from the dirt entering his mass of wounds on his back as well as his dislocated shoulder and revealed collar bone.

"Oh, God…John… I'm so sorry…" Elizabeth cried as Beta approached the couple with the cover of four members of her personal guard. Elizabeth looked up to them as John now lay unconscious on the dirt ground, with his damp head on Elizabeth's lap.

As they stopped, Beta turned to one of the guards around John and Elizabeth and spoke tonelessly, "Dial the Atlantis Stargate,"

Elizabeth looked up, and sniffed. "What?"

"The Colonel is to be returned home- he is of no use to me or my people any longer so he will return to your world where he may or may not recover; It depends on how good your doctors are."

Elizabeth gripped John's limp hand in hers and swallowed. "And what about me?"

"I am afraid you must stay a little longer but you shall not be harmed; you have a few moments to say goodbye to him before he returns to the city of your ancestors."

Beta nodded to two of her guards as she turned and stalked back to her mansion which was situated at the edge of the encampment- the two guards remaining to take John away.

Elizabeth sniffed and brushed her hand through his damp hair as she spoke to him in a quiet voice, "John… I love you… Please, don't give up… Just hold on and Carson will make everything right… I'll see you soon…"

"'Lizabeth…" John murmured weakly as he attempted faintly to grip her hand in return as he swallowed, opening his eyes open slightly. "'give me… Love you..."

"There is nothing for you to be sorry for," Elizabeth replied, trying to put as much strength behind her words as possible, as the guards came over and bent down to grab John's arms, pulling the Lt. Colonel upright which caused him to yelp and pass out as the combined pain became unbearable, releasing Elizabeth's hand as two more guards who had been standing nearby came to hold her back as she fought to get to John as the two guards roughly dragged him to the gate.

"No," she cried. "John, No!!"

**--**

The two guards dragged John's unconscious and broken form to the now active Stargate. One guards forcing John's limp fingers to put in his IDC Code that would lower the Atlantis shield, before going up to steps and shoving the injured man through to the ancient city and to a shocked gate room….


	2. Chapter 2

**Chapter Two: A Medical Emergency**

--

"Unscheduled Off-World Activation!"

Colonel Steven Caldwell came up to stairs to the Atlantis control tower to where Dr. Rodney McKay was looking at the data that was showing on one of the laptop screens. "Doctor,"

"We just received Colonel Sheppard's IDC and the shield lowered itself."

"Doctor raise the shield, it could be a trap."

"Let me rephrase that, Colonel, we cannot raise the shield because we do not have any control over the system."

"Well how is that possible, Doctor?" Caldwell asked sceptically.

"How should I know?" McKay shot back.

Caldwell spoke into his radio, "Security team to the gate room."

As the security team led by Major Lorne came into the gate room, they positioned themselves strategically around the gate followed by Teyla and Ronan, who waited with the marines anxiously as the event horizon shimmered, the team looked on in horror as John Sheppard came barrelling through the stargate, tumbling down and leaving a trail of blood behind him as he landed in a heap on the smooth floor.

Rodney immediately rushed down the stairs, meeting Teyla and Ronan as they ran to the unconscious man who had his back to them. Teyla bent down to him as Lorne spoke into his radio urgently.

"Medical Team to the Gate Room, STAT!!"

Teyla felt bile rising up at the back of her throat as she reached John's lifeless form and after turning him over, saw a piece of John's collar bone through the ripped flesh on the front as she checked for a pulse which she did not expect to find.

Ronan looked at the mess Sheppard had left in his wake- His anger intensifying- as Rodney stood just behind Teyla as Beckett and his world class medical team arrived but none of them were prepared for the state of Sheppard's bare upper torso.

It was a mass of open wounds thanks the cat-o-nine tails with blood seeping onto the floor and forming a pool of Blood around him and around Teyla, who looked up to Beckett who had come over to them immediately.

"He is alive, Doctor," The Athosian leader whispered as Carson swore to himself.

"Bloody hell, Get him to the bloody infirmary NOW!!"

Beckett and his team laced Sheppard on a gurney and whisked him off hurriedly to the infirmary to begin hours of treatment before his team could see him and perhaps two weeks at least before his team could get anything from the injured man about what happened and whether Elizabeth was even alive.

For the meantime however, all the team and the rest of Atlantis was hope that John was tough enough to get through the kind of trauma that even the most experienced personnel had never experienced.


	3. Chapter 3

**Chapter Three- Wanted**

Elizabeth lay curled up on the four poster bed, not moving from where she had lain after two of Beta's guards brought her to the female avatar's "home" and to this Victorian style room which was well furnished with clothes lain out for her on a large couch.

But the thought of all this comfort made her feel sick- she had no idea what would happen to her and all she wanted was to go home and be with the man she loved who had suffered for the both of them.

Elizabeth had never gotten around to tell John that she was six months pregnant with their third child- The two Atlantean leaders had married five years ago after having their oldest son Scott who was eight and also now having a two year old son, Cameron.

Elizabeth wasn't showing any sign of pregnancy and Carson Beckett was the only person who knew about the new, soon to be, member of the Sheppard-Weir family- After falling pregnant with Scott when she and John were still keeping their relationship a secret from most of the city, Elizabeth ha confided in the Scottish doctor and had told him everything. Now she hoped that the doctor would tell John about the pregnancy, giving the injured man something more to hold on to so he could get better for both of their sakes; Carson had discovered the sex of the baby, but at Elizabeth's own discretion put it down on her maternity chart as Elizabeth wanted to keep it a surprise. All she had wanted to know was whether the baby was healthy and Carson gladly informed her that she and the unborn child were completely healthy.

The old fashioned oak double doors opened and Elizabeth turned her head to see Beta enter the room. Ushering her entourage out, the avatar wanting the two of them to be alone.

Elizabeth lay her head back down and placed her other hand protectively over the area where her unborn baby grew healthily and unaware of what was going on.

"Dr. Weir, you should eat something… For both you and your unborn daughter"

Elizabeth couldn't help but turn around to face the female Avatar who sat in an oak chair beside her bed.

"What did you say?" she asked, barely audible, as Beta put her fingers to her mouth which had curved into a slight smile.

"You are having a beautiful, powerful little girl- Did I spoil the surprise? I know that most parents wish to keep the gender of their baby hidden but female Avatar have the ability to sense the life within… It is the reason why you are still here."

Elizabeth sat up on the king sized, four poster bed and moved away from Beta who watched Elizabeth with a look of amusement as the mother went to the edge of the bed and brought her knees up with her hands pressed over her baby protectively.

"Why are you doing this? What do you want?" Silently praying that the answer she had made in her own mind would not be so.

Beta brought her hands down and smiled warmly, which gave Elizabeth the dreaded answer she had believed and which brought more fear than she had ever felt from the wraith or the genii.

"We would like your baby," she said simply.


	4. Chapter 4

**Chapter Four- Losing Them Too**

"Elizabeth… Elizabeth!"

Carson Beckett came out of his office and went over to the infirmary's sole occupant who, after a week of heavy sedation, life support and round the clock care, had been making slow and steady progress- still having a long way to go- but he was having nightmares.

After almost two weeks of being under heavy sedation for all the severe lashes and malnutrition plus the added bonus of many long hours of surgery to repair torn tissue an relocation of his right shoulder- which was now immobilised and had been stitched u with likeness of scarring- John Sheppard was progressing slowly.

Carson tapped John's cheek lightly in order to wake the soldier but the injured man tossed and turned as the doctor tried to awaken him and bringing him out of his nightmare. His brow was furrowed as a thin layer of sweat formed on his bare skin as he began to mumble incoherently as the doctor touched his left shoulder lightly as he called out Elizabeth's name again and again.

John grunted softly and tensed under the doctor's feather light touch, stretching all of his stitches which had taken almost ten hours due to the abdominal bleeding and large amount of blood loss which he had sustained during his day of punishment, the colonel was in hospital scrubs and attached to a variety of monitors registering his heart beat, pulse, blood pressure and O2 levels as an IV line fed him medication and hydrating fluids into his healing body.

"Colonel, John?"

John's eyelids fluttered for a moment as he opened them slightly as he felt a nasal canula as it fed him oxygen and also the IV line snake up his bare arm. He lay on his back and was being slowly having a reduction of Morphine which he had needed because of the severity of the pain for the first week, still having an ache from his back and shoulder especially.

Swallowing hard, the Lt. Colonel turned his head to see the worried look that Beckett was giving him; the same look that each member of his team had given him when they had come to see him continuously over the past two weeks and he inwardly hated it- sympathy and worry. It made him feel weak and that was the last thing he needed. Scott and Cameron had come to see their father everyday- Just as Rodney, Ronan and Teyla's children had- and, as John had discovered from Carson when he had awoken, the two boys would fall asleep on his bed so after the first few days, the nurses had given up on moving them onto the next beds but had put the bars up on the bed so that they could stay with their father without ending up in the infirmary also.

All of the expedition's children- and particularly the teams own- idolised the pilot who would often play with many of the youngsters whose ages ranged from Cameron at Two up to Eight for Scott and Riana and would often take the children on flights to the mainland and back for days of play even when he had duty rosters to do and mission reports to complete.

"Colonel, can you here me… John?"

"Where's Elizabeth?" he asked in a hoarse voice that was barely a whisper as Carson gave him an ice chip in order to moisten his mouth, allowing the coolness to wash down his sore throat which etched as he spoke.

Carson avoided the soldiers eyes and the question because he didn't want to upset the Lt. Colonel and slow his recovery even more and thus, their only hope of finding Elizabeth. From the bed, John watched him.

"Carson,"

"I'm sorry lad," Carson sighed. "You're the only one who came back."

John turned his face back up to stare at the ceiling as he tried to remember how he managed to get back without Elizabeth. Images flashed in his mind as he remembered the punishment…

Seeing Elizabeth holding back tears…

Being released and being turned over, his head being placed gingerly on a soft lap…

Through his coldness, a soft hand brush through his hair as he opened his eyes and saw Elizabeth's tear stained eyes as he asked her forgiveness before he slipped into darkness…

Having dreams of Elizabeth, his young sons, his team…

And strange young girls who he seemed to have fun lifting up and spin her around laughing as he brought her down to him and kissed her brown hair which lay in two cute pigtails as she put her small arms around him lovingly…

'_She is pregnant with your child-'_

Beta's voice echoed in his mind as he remembered the little girl of four or five years of age…

'_It's a shame you will not be able to see your little girl grow up...'_

He had watched as the little girl vanishes from his arms completely…

John felt Carson's worried eyes on him at the long pause as he spoke hoarsely, still looking at the ceiling.

"She's pregnant," he turned to Carson, "Elizabeth's pregnant isn't she?"

Carson sighed. He knew the Lantean leader to well but something must have happened to him having found out. "Aye Lad, I'm afraid she is."

"A girl?"

Carson looked into his eyes "Elizabeth didn't tell you so how to you know?"

John sighed, wincing as he shifted position slightly to try and work his tired muscles, stiff from misuse. Taking in a long shallow breath.

"I found out the hard way- She hadn't expected me to survive."

"Elizabeth?" Carson asked, surprised.

"Beta… The avatar who took us." John croaked. He turned back to the ceiling, "We escaped but… but we got caught just as we were reaching the gate… before my 'punishment' Beta told me that Liz was pregnant and I wouldn't see our little girl grow up."

"she is expecting a little girl," Carson confirmed solemnly. "but she didn't want me to tell her the sex of the baby- she didn't expect to be pregnant again so she wanted it to be a surprise."

"Beta's only keeping her for the rest of the pregnancy… then she's gonna take our little girl and probably kill Elizabeth if we don't get to her." John closed his eyes and asked, "How far gone is she?"

"You may have noticed her beginning to wear baggier clothes- She's about six months; I don't know for sure… I took a scan and their both completely healthy which is a good thing… You've been having nightmares, haven't ye lad?"

"What makes you say that?"

"You've been calling 'Lizabeth's name over and over again."

John fidgeted with the blanket as he allowed an uneasy silence to ensue before changing the subject.

"Where are the boys?"

"I don't think you should see them right now- This is only the second time you've woken up."

"I need to Carson- I need to see they're okay. Please."

**--**

Teyla Emmagen-Dex stopped beside Carson as Eight year old Scott and Three year old Cameron hugged their father as he kissed their foreheads as he used his left hand to ruffle the boys short brown and dark hair as the two boys talked to them excitedly as John listened to them with a weak smile as he listened to them with a weak smile as he responded quietly but Teyla and Carson knew otherwise.

"He will attempt to go back for her, even in this condition… for the boys and because he loves her more than life itself." Teyla told the Scottish doctor as they watched the exchange from Carson's office.

"I'm afraid it's more than that lass," the doctor sighed. "Elizabeth's pregnant, and the bloody nutter who took them wants the baby."

**--**

After John woke up the next day, Carson came over to check on his patient's progress and to bring him his lunch tray. He saw the look on John's face which had showed after the storm and after saving Elizabeth from the nanites that had taken over her mind and knew what was coming.

"Don't even bloody think about it because your not bloody going on a suicide mission."

"Doc,-" John began to protest weakly, putting his knife down.

"Don't you bloody 'Doc' me, Colonel, I just patched ye up so I don't want to find myself doing that again anytime soon do ye hear me? Just wait until your strong enough to go saving the bloody world again."

John put the fork down in mild frustration, "Carson, I can't lose them, I won't lose them. If I have to play the hero and go back there tomorrow I will- with or without your help; I can't leave Elizabeth… or our little girl."

"You're gonna' make this difficult, aren't you lad,"


	5. Chapter 5

**Chapter Five- Rescue Gone Wrong**

--

-**Dream**-

_He opened his eyes, taking in a deep breath and exhaled slowly out, taking his time to wake up as the sun came through the stain glassed windows which had opened automatically a few minutes before, which allowed in the fresh ocean air._

_John Sheppard turned his scruffy dark haired head to see Elizabeth asleep with her face toward him, one hand under her head while the other lay across the sheet to touch his thigh lightly. John smiled as he felt a smaller body between them and looked down to see a three year old toddler lying in between her parents, sleeping blissfully with Elizabeth's arm over her with John's own around the little girl who had her head on his shoulder- her face tucked into his chest contently- with her little thumb within her partly open mouth. John smiled tiredly as the colonel brushed a wisp of her short brown hair off of her rosy cheek with the blanket around her waist._

_Elizabeth's leg brushed against his lightly as she began to wake, moving her hand up to her face to rub her eyes as she brushed her other arm lightly over their sleeping daughter, who snuggled closer to John's body as he brought his arm around the little girl comfortingly as her mother rubbed sleep from her eyes as she heard a hoarse voice,_

"_Good Mornin'"_

"_Hmm," Elizabeth murmured as she opened her hazel eyes to see her lover's slightly glazed blue-grey coloured eyes, "Morning…"_

"_Look's like we've got a stow-away here," John groaned lightly, brushing his yet unshaven face lightly against their three year-old daughter, planting a kiss in her hair as Elizabeth brought her own hand to the little girl's hair and brushed it lightly._

"_She's her daddy's girl," Elizabeth mused tiredly as John leant over and planted a reverent kiss lightly on her lips._

"_I just wish she could stay like this forever," John countered as he felt the small body in between them shift as the three year old yawned as she took her small thumb out of her mouth and draped her arm across her father's bare chest, touching the scar over his collar bone._

-**End Dream**-

--

"Colonel, is everything alright?"

"Sheppard?"

"Wh… Oh yeah, let's go."

Teyla and Ronan brought Sheppard back to the situation at hand, realising that the other occupants of the puddle jumper where looking at him.

The team had returned in a cloaked jumper to Beta's prison world where Elizabeth was still being held. John was still unsteady on his feet but was stubborn and had talked Rodney, Carson, Ronan and Teyla into helping him get Elizabeth back.

**--**

Beta walked down the corridor to Elizabeth's quarters to check on the expectant mother. A few days ago the human woman had been given an injection that would shorten her pregnancy; her fellow avatar were growing impatient and wanted the child.

Nodding to the guards at the door, Beta entered the room to find Elizabeth curled up on the bed as she was every time Beta came. The Atlantean leader was looking out of the window to the Blue Coloured sky and was humming something to her unborn baby.

She had begun to feel tightness in her stomach, not noticeable most of the time but now it was becoming more and more painful and they felt like mini contractions that were slowly growing closer together and more painful the closer they became.

She had been thinking about names for the little girl growing inside of her healthily each day. Elizabeth wanted the baby to feel safe even if Elizabeth, herself, knew they were not- Sometimes she thought the baby knew what she was she was thinking using her movements and kicks to reassure her mother.

"How are you Doctor Weir, I trust you and your daughter are well today."

Elizabeth closed her eyes and wished she was back in Atlantis, hearing the ocean from her window as she lay in the lovely double bed she had shared with John.

John… her heart skipped a beat as she began to silently choke back tears at the thought of him being dragged off unconscious, blood drying on his back which had become a mass of open wounds- he hadn't even fought back when they had plucked him from her limp arms… Beta's voice brought her back from her memory.

"We'd be better if we could go home and to try and see my husband is alive or not."

Beta smiled, clasping her hands together in front of her, a smile playing teasingly on her lips, as she watched Elizabeth's body tense as another contraction came on causing Elizabeth to moan.

"I see your contractions are becoming more noticeable, I think that we shall see your daughter by the next evening."

Elizabeth's eyes widened, finally realising what the injection she had been given truly was.

"you… you forced me into… into premature labour. Why? It's not safe."

"My people are becoming impatient and we want that child before your friends arrive."

"They're coming?" Elizabeth whispered, barely breathing.

**--**

"Don't you think that ye should slow down there a bit John? You've only been up and about for about a week."

"Reprimand me later Doc, I've got a wife and unborn child to save here." John said as he shifted his P90 lightly as the team went on at an unforgiving pace.

The team followed John as he led them through the light filtering trees through the forest where he and Elizabeth had hidden in almost a month ago now when John had no knowledge of his daughter.

"You seem to know where you're going Sheppard, come here a lot?" Dex asked as he drank in the surroundings; every shadow, every little detail and every rustle of leaves ready for anything and holding his magnum gun low but ready for any sort of ambush.

"Yes Colonel, how do you know where you're going?" Teyla asked curiously as she walked with Carson and Rodney just behind John, Ronan bringing up their six.

--

_-_**Flashback**_-_

"_Come on, we have to keep going just a little longer."_

"_I can't run anymore John, I'm Tired."_

_John slowed to a stop, bringing Elizabeth- who had been holding his hand as they ran- to him and slid down to the ground with Elizabeth's head under his chin. They had been on the run for almost eight hours, not stopping for a proper rest because of the guard perimeters on the planet and because they were heading toward the stargate._

"_Okay, okay. Let's have a break." John said, catching his breath as he rubbed his hand up and down Elizabeth's arm which felt cold as he felt a shiver run through his wife at the cold night air- the forest putting a feeling of dread on them._

"_How long will it take us to get to the stargate?" Elizabeth asked, weariness etching into her voice after not taking a long break; John had only allowed them a minute or two before having to run again from the patrols near the gate and clearing close by._

"_I don't know. Dodging the guards and hope not to get caught on Beta's guards which would lead us to her bad side- Two or three days if we do this real carefully."_

"_I just want to go home and see the boys, they might think we've abandoned them." Elizabeth murmered, nuzzeling into John's chest and being soothed by his steady heart beat._

"_Don't worry, the guys will take care of 'em."_

"_I hope so."_

_-_**End Flashback**_-_

--

"Colonel?" Teyla's voice brought John back to the situation at hand.

"Sorry, er, Liz and I went on the run to try and get to the gate and we were here for almost a week so I know this area pretty well."

John halted suddenly which caused the rest of the team to do the same. Using a signal, they went into cover as a patrol of two of Beta's guard came through the dense vegetation.

"Dammit," Sheppard cursed as he got up again, the team doing the same, and carried on more carefully through the forest as they heard voices coming from the direction they were headed.

"What? What's the matter?" Rodney asked as he fumbled for his 9mm in his thigh holster at Sheppard's sudden change of tone.

"I think we're in trouble," Was all the colonel said as five bursts of light erupted around them, "Oh Crap,"

John convulsed as the light hit him, causing him to crumple to the ground. Ronan started to shoot in the direction of the bursts but he soon followed Carson, Rodney, Teyla and John in a crumpled heap on the ground as a group of Beta's guards came out.

The leader nudged John, turning him on his back.

"Beta was right," he muttered as he turned to his patrol. "Take them to her."


	6. Chapter 6

**Chapter Six- Saving Mommy and Daddy**

--

"It will not be long now m'lady,"

The servant girl said, looking from Elizabeth's lower half where her body was getting ready for the birth of her daughter. Elizabeth was breathing heavily as she relaxed after another painful contraction passed, leaving her breathless.

"You cannot take my daughter, I won't let you ," She murmered, her head on the pillow.

"You do not have a choice in this matter, Doctor, you would never be able to look after this little girl properly- you cannot begin to comprehend even a small amount how powerful she will be."

Beta brushed Elizabeth's comment off as if the doctor had never even spoken.

"Ah!" Elizabeth cried as she gripped the bed sheets as another contraction came on, the servant girl- Marin- used a damp cloth to patt Elizabeth's damp forehead.

"I love her," Elizabeth gasped as she fell back onto the pillows. "Her father loves her, that's all that matters. It doesn't matter if she has powers or if she is normal… she's our daughter and you can never… NEVER take that way from her or us- we have a connection that can never be broken."

"You believe so?" Beta asked curiosly as the doors suddenly swung open, causing the avatar to spin around, her face showing a look of fury. "WHAT IS THE MEANING OF THIS!?"

The lead guard entered as his men dragged in the unconscious Atlantean team, Beta's furious gaze turned into an evil smile as John was dragged in finally- the team falling into heaps on the floor at Beta's feet as the guards covered them closely.

Beta smiled, stepping aside as to allow Elizabeth to get a clear view, her gasp made Beta even more amused.

"John-Ah!" Was all the expectant mother could get out as another contraction suddenly overwhelmed her.

The sound caused the team to slowly come around, Ronan and John waking first and immediately regretting is. One of the guards came over to John- An old acquaintance- and dragged him to his knees roughly, causing John to close his eyes as dizziness overcame him, hearing Ronan growl as he was given the same treatment.

"Well, it seems that you are stronger that I ever thought you could. You have managed to surpass my expectations regarding human endurance- I congratulate you."

Beta clapped her hands lightly in sarcasm as Elizabeth's heavy breathing filled the silence as Rodney, Teyla and Carson came to from the stunner's effects.

"Oww, my head. I think I have brain damage," Rodney groaned as he and his team mates were brought to his knees.

"I hate to disappoint you, Beta," John groaned as he adjusted to see the new situation, "You miss me that much, huh? Couldn't live without me?"

"John, you're… you're here…" Elizabeth murmered tiredly as she battled exhaustion; there was a measure of uncertainty in her voice as if her were only a dream.

John fought the guard, his shoulder and back screaming in pain as he resisted their restraint upon himas he told Elizabeth with a mixture of lov and desperation.

"It's me and I'm not going anywhere… I promise. I'm gonna be right here for you… and our little girl."

Elizabeth allowed herself to show emotions now; emotions that she had hidden well but after hearing his voice, were overwhelming her as she tried not to cry. Her happiness was short lived as another more painful contraction came on and she cried out once more. Carson looked over to the bed and then to Beta.

"I'm a doctor, I can help her. Just let me go over to her."

Carson said in his doctor tone of voice. Beta thought for a moment but nodded to the guard holding Carson to release the doctor. Carson immediately went to Elizabeth's side and began to examine her progress. It soon became evident that he was not pleased.

"Lass, this wee girl is too early for my liking,"

Beta cut in before Elizabeth could respond.

"You continue your activities Doctor… Beckett, my people are anxious for this baby to be born as soon as possible if in the hope to have a chance against her fellow phoenix friends who are after us."

John struggled even more. "What the hell are you talking about, she can't help you! She's just a little kid, she didn't ask anyone to make her special!!"

"Now, how would you know that she was special Colonel? As far as I recall, you were half-dead and in the precious ancestral city you hold in such high regard while your wife was worrying about you."

"If touch my wife or my daughter… I will kill you," John snarled as Beta came over to him as once again dragged his head back by his hair roughly, causing Johnto grunt through clentched teeth.

"You think so human? Many have tried and they have all failed… You may have survived last time but this time I shall watch as your blood lines the floor of this room."

Ronan, Teyla and even Rodney began to struggle at the comment, knowing that this wasn't a good sign as Carson went forward but was blocked. Elizabeth was now beginning to cry as the situation escalated.

"If it means that my daughter is kept away from you… you can kill me all you want," John muttered through clenched teeth, his guards pulling him upright.

Beta turned away for a moment- pulling from her robe a shiny athame- before spinning around and plunging it deep into John's abdomen, going straight through his vest asd causing a mass of internal bleeding. John gasped as he took in air but regretted it as the guards released him and he doubled over- the knife still buried in his stomach- as he was held by Beta, who turned it within him- causing the soldier to yell- before pulling the now blood stained knife out quickly and smoothly as John collapsed instantly and landed on his back on the floor before turning onto his side with his face to Beta who- for good measure- kicked him ferociously.

"John! John no!" Elizabeth cried as she tried to move but was stopped by another, more painful contraction. Beta- knife still in hand- moved toward her.

"This is taking too long. Deliver the baby, Doctor, or it will be you who shares the same fate as it's father."

--

Maternity doctor's encourage mother's to talk to their unborn children as the child can pick on words as well as feelings and emotions. The baby inside Elizabeth picked up on her mother's emotions as she heard her mother cry; the emotions were so overwhelming that the little girl thought she should somehow reassure her mother.

--

Elizabeth felt the sudden change in her baby almost immediately, seconds before what was about to happen; she felt a surge of energy course through her body- removing any tiredness or exhaustion she may have had moment's ago.

Beta also felt the change in Elizabeth and the little girl and spun around from John's feeble body as John and Elizabeth's baby made their prescence known to everyone in the room.

A surge of energy burst out into the room, causing Elizabeth to cry out in shock as it rose out of another contraction; the baby using telekinesis to throw the guards holding the team and standing about the room hard into the walls, out of the door, and two smashing through the window.

--

"Oh My God," Elizabeth cried in shock.

"What was that about? Bloody Hell!" Carson swore as he turned to Elizabeth who turned her head to him in shock. "Lass, what's the matter?"

"My water's just broke," She whispered as the baby sent out another, much more forceful message.

-She is more powerful than Alpha Foresaw-

--

Beta thought as the little girl used her powerful telekinesis to lift the guards up once more and chanelling her mother's untapped raw emotions; Fear, Anger, Compassion… Love- and making them even more powerful as she unleashed her mother's fury- and feeling other people's raw emotions- combined them as she sent out a much more destructive wave upon Beta's loyal guard.

A wind rushed through the room as Teyla, Rodney and Ronan went to John's side as he watched the scene unfold through heavy eyes as Teyla gently lifted his head off the floor and onto her lap as he covered his stab wound with his shaking hands which were shaking uncontrollably-and paled- with stark red on them from the seeping blood.

Beta and Teyla's haired flew back as the wind strengthened in the room as the guard- who had come to- began to scream in pain as the little girl unleashed the combined emotions of her mother and those she cared about and began to break down the guard's molecular structures- Their bodies… Their individual cells- and began to turn them into a fine ash that appeared dark grey in colour.

The ash soon began to swirl around as the guards were decimated with a force greater than that of a Super Tornado but which didn't seem to affect the Atlantean team and Marin; who was now cowering against the wall beside the four poster bed Elizabeth was lying on-gasping for breath at the power.

The guards screams of terror sooned died away as the last of their bodies disappeared into a tornado of ash swirling in the middle of the room, before appearing to blow up and disappear all together with nothing left.

As residue energy remained, the little girl chanelled that to where she felt the greatest pain- to John.

--

John gasped as he suddenly felt the power enter his body and flow within him; within a few moments the pain from his wound vanished and he felt better than a moment ago. He knew something was different when even Beta's face became a mask of surprise.

"How is this possible," The avatar voiced aloud.

-Not even Alexial or Xaphania have the power contained in this young girl-

--

John sat bolt upright, one hand supporting him on the floor with the other around the area where his stab wound had been only a few moment's ago; his breathing evening out as he looked up to Beta, whose facial expression turned to anger.

"What just happened?" He asked, looking to Beta, who in turn looked to Elizabeth- her blood stained knife still in her hand- and purposely went over to the bed.

"No," John growled in realisation as he got up - the only pain he felt was now coming from the original places- and went at Beta in a leap but was throw back into the wall by an electric shock and slammed down hard onto the remains of a table, unconscious.

Ronan picked up a weapon which had belonged to a guard and aimed at the female avatar, "Try this,"

He fired the weapon but it exploded as if hitting an invisible wall surrounding the avatar.

"If we cannot have your child alive, then both of you will die together," Beta said as Elizabeth's fear showed openly as the lantean leader attempted to move away but another contraction timed in and the doctor screamed at the pain and cried.

Carson looked on and muttered to himself. "Come on ye wee lass, do what ye did before."

Elizabeth put a hand over her bump protectively- feeling much more drained now and knew the baby was probably exhausted after saving them- as Beta neared, her knife held high when something bizarre happened.

--

Beta felt her body begin to disappear as she was summoned away by a strange force.

"No," She screamed. "The child killed my most trusted guard, she has already manifested powers we cannot hope-"

But her words dissipated as she vanished,leaving the team and Marin.

--

Elizabeth was safe but now they had more pressing matter's.


	7. Chapter 7

**Chapter Seven- Back Home**

--

"Alright Lass, ye wee girl is in distress so your going to have to push for me- one big push."

Another contraction came on, causing Elizabeth to cry out at the intensity of it. John, lying next to her on the puddle jumper's floor, squeezed her hand tightly in reassurance as Beckett had told the colonel to remain lying there after coming round a few minutes before from the electrical shock he had received from Beta- all the while Teyla aided Beckett in anyway she could with the two Lantean leaders.

Ronan had carried Elizabeth to the cloaked Jumper as Carson, Teyla and Rodney helped John to reach the clearing; Leaving Rodney to fly the ship with Ronan riding Shotgun as Elizabeth had no choice but to follow Carson's careful instructions to ensure the safe delivery of she and John's now distressed baby.

"Ah, I can't… I can't."

"You have to Lass, you're almost there, one big push."

"I'm here, you can do it,"

John's words brought some comfort to Elizabeth as she gripped his hand even more tightly as she cried out, putting her exhausted body to the limit to deliver the little girl who had just saved all of there lives- Especially John's- and when she felt that she could push no more, Elizabeth sagged against John as he held her to him comfortingly as Carson carefully held the newborn in his arms, covering her up in his jacket.

"You have a healthy, beautiful little lass."

Teyla and Ronan shared a look and a smile as Carson brought the little girl to her parents. Elizabeth turned her tired green eyes to John as Carson gently removed his hands, John looking down in a childish-wander as Teyla turned her gaze to the little girl with a warm and gentle smile.

"Look at what we did,"

Elizabeth cooed tiredly as she held the small baby while leaning into John's chest after the soldier had pushed himself up against the back wall of the Jumper; his face was once again becoming pale with a thin layer of sweat forming on his forehead, yet he refused to show this weakness until they had returned to Atlantis- with the knowledge that his family was safe, as John planted a kiss into Elizabeth's damp curled hair.

"Yeah, I do. She's a little miracle." He agreed as fatigue began to settle on his weary and still recovering body.

Carson noticed John's deteriorating condition, and gave the soldier a worried glance, which John ignored as he put all his energies nto focusing on his wife and new daughter, who wriggled in her makeshift blanket; her eyes still closed, but crying her eyes out at the top of her lungs, wanting to be the center of attention.

"the medical team are waiting in the Jumper Bay," Rodney called over the crying, still shaken by what had occurred as he sent the IDC through to Atlantis and flew into the stargate- coming out seconds later and going immediately up to the Jumper Bay as the medical team waited patiently with two gurneys for John and Elizabeth.

As the Jumper hatch lowered, Elizabeth noticed the two gurneys and gave Carson a questioning look.

"Our original patient has taken a turn for the worst after his recent excursion."

He nodded to John whose eyes were now closed as he leant his head against Elizabeth's; his breathing was once again becoming shallow and uneven as he used his remaining strength to hold Elizabeth close- letting exhaustion, pain and his original injuries overcome him as they sapped every last ounce of energy he had left.

Elizabeth was about to speak but Carson silenced her. "Don't worry, he'll be alright with time. Let him rest."

Elizabeth merely nodded.

With everything that had happened in the last few hours- from their daughter's birth and the team's rescue- her mind was beginning to clear as she remembered what John had been through only a week-and-a-half ago and realising that in order to mount a rescue, John would have gone against Caldwell and had risked his own recovery by forcing his team to follow his lead to mount the rescue.

Remaining silent, as she held the new arrival- who was now merely gurgeling in understanding- as a medical technician gently removed John's arm as they laid him down on the Jumper floor-while another helped Elizabeth to sit on a Gurney- and aided Carson who was now having to give John a new IV line immediately as he was told the Colonel's sats had dropped and his respiratory was almost non-existent as a Defibrilator was brought in and Carson used them on the Military leader several times before he returned to them and ordered the technicians to place him in Intensive Care immediately.

Elizabeth was being supported by Teyla as the Doctor with them suggested that they take the new mother and daughter to be checked over so that the medical team could do their work.

"They'll do everything they can, Doctor Sheppard, but we need to check you and your baby out," Doctor Nichols- a new member of the medical staff who had been reassigned to the Atlantis expedition- explained gently as Teyla nodded slowly in understanding as the three women were joined by Rodney and Ronan; both of whom remained silent as they too watched Carson work his magic on their CO and friend.

Elizabeth did not remove her eyes from John as she was slowly wheeled away- vaguely aware of Ronan saying he would remain with Carson and John- as she held the newborn who had fallen asleep during the commotion more securely, knowing that the female doctor was right- Only Carson could help John now, and Elizabeth had to stay on form if she wanted to be able to look after her husband and newborn child in particular over the coming week or so in the infirmary.


	8. Chapter 8

**Chapter Eight- Touch and Go**

--

"I need an ventilator pack and IV Anti-Biotics Stat,"

Carson barked as he rushed into the infirmary at the side of John's Sheppard's still form which lay still on the gurney which was being pushed into one of the resusitation room which had been set up almost Twenry years ago as the Infirmary expanded as more resources became available from earth thanks to the Midway Gate System which now linked Atlantis to Stargate Command with a mere thirty minute travel time.

Cutting away Sheppard's black t-shirt, which had become blood stained as the whiplashes opened up with avengence and his body began to shut down through exhaustion, Carson immediately checked the area where the Colonel had been stabbed by the Avatar only to find a thin scarline which was still an angry shade of pink but all the same, healed.

"Doctor?"

One of the nurses asked questioningly as Carson gently ran his hand over the wound, feeling John beginning to shiver under his touch as a new fever began to course through his veins- the wounds had been infected and the only reason the infection had been contained was due to the regular doses of Anti-Biotics, but that was now no good as the fever was made worse by John pushing his already injured body beyond it's own limits.

"It's nothing Lass," Carson nodded distractly as he called out. "I need a new course of Anti-Biotics for suspected pneumonia and I need to get the colonel into surgery again pronto."

**--**

Ronan Dex walked wearily into another part of the Infirmary after just leaving John, as he was rushed to surgery to repair the healing wounds which had been reopened during the last mission from being thrown about on the planet by Beta and her guards, and going to where Elizabeth, Rodney, and his wife Teyla had been taken to as Rodney and Teyla remained with Elizabeth and the little girl who, Ronan discovered, Teyla was now holding.

Elizabeth was now attached to an IV also in order to gain some lost nutrition and to give a blood transfusion after the amount of blood she had lost while giving birth to the young girl and who had been diagnosed by Doctor Nichols as being slightly anemic.

Teyla was the first to see the Satedan as he came through into the quieter area of the infirmary levels where his wife and friend stood around a now lightly dozing Elizabeth who now wore white hospital scrubs and who had a nasal canula to give her some extra oxygen after her over exertion a while before.

"Ronan, how are things?" Teyla asked quietly as she took her eyes away from the sleeping girl she held securely in her arms, Rodney hearing the question looked up also.

"He's gone back into surgery, his wounds opened again and Carson thinks he's been hit with another bad infection- it's touch and go. He's on a ventilator now." Ronan said heavily as Rodney looked cast down as he turned away with his head bowed before looking up to Elizabeth who now slept but with an obvious frown line on her forehead.

"He is in the best place, Rodney; Carson will make sure the Colonel comes through- just like before. What about the stab wound he sustained from the Avatar?" Teyla asked, the scene suddenly flashing before her brown eyes.

Ronan Shrugged.

"Gone. All that's left from what I can tell when the Doc was checking out the area, there's nothing' there but a small scar."

"Really?" Rodney said, suddenly perking up at the news after seeing all the blood gushing from the wound when he had come to Sheppards side.

"That is… good to hear… she is truly a… miracle." Teyla remarked cautiously as she looked down to the girl in her cradling embrace as Elizabeth stirred behind them after hearing voices.

Opening glazed Green coloured eyes, Elizabeth found that the lights were dimmed so she was able to open her eyes without being blinded and slowly turned her head to see the slightly blurry silhouettes of Teyla and Ronan as they stood next to Rodney, who sat on the stool beside her bed.

"John?" She queried, as if this where just a dream and that she was, in fact still in the Avatar's hellish encampment.

Teyla, Ronan and Rodney turned at her quiet plea and immediately went over to her bedside. Elizabeth's vision cleared even more as the three team members came over, and she saw Teyla holding the little girl in her arms, and noticed the looks on their faces which caused her to sit up straighter in the bed.

"How are you feeling?" Teyla asked gently as she sent Elizabeth a weak smile.

"Where's John?" Elizabeth said, much more strongly as Teyla lowered her eyes as she turned to her husband.

"He's in surgery. They're trying to repair the re-opened lashes Sheppard aggravated." Ronan said a-matter-of-factly as Rodney rolled his eyes at the frankness of the Satedan.

"Oh My God." Elizabeth whispered as Teyla glared at her husband before handing the little girl to him, causing the Satedan ex-runner to fumble momentarily as he shifted the baby into a secure and comfortable position in his arms, as the Athosian came over and placed an arm around Elizabeth's shoulder.

"He is in the best hands, Elizabeth; he will be fine once his injuries are sutured once more and he is given the time to recover properly- He would not rest until we agreed to aid him in his rescue mission and even then…"

"He wouldn't let Carson boss him around on the planet either… And the state he came back from there in the first place was a lot worse than now…" Ronan put in helpfully as he awkwardly bounced the sleeping baby.

"Not helpful, Ronan," Rodney put in sarcastically as he rolled his eyes and slapped his hand on his leg exasperatedly.

Elizabeth just sat there, allowing Teyla to hold her as her shoulders began to shake and sobs began to erupt from the back of her throat as tears began to shed. All the Athosian Leader could do was hold the woman as she cried for her lover- Teyla guessing that she had not dared do so back on the planet incase they showed weakness- and the possibility of him not making it through to see another day.

**--**

The gurney was wheeled into the infirmary's Critical Care bay by two medical technicians, who locked it into place as Carson Beckett took off his surgery scrubs and gloves as he followed the gurney which had John Sheppard laying still and unmoving atop of after the four hours of surgery to repair the damage from re-opened wounds and new abrasions newly gained after the last rescue mission.

Laying Bare Chested with the sheet pulled upto his waist and attached to a ventilator and IV, John Sheppard looked like he was losing the fight as the machine appeared to be the only thing keeping the Colonel alive at the moment in time.

His temperature had reached almost 100 during surgery and it remained dangerously high even now as Carson asked for John to be placed on a higher dosage of IV Anti-Biotics and Pain-Repressents to keep the playing field even.

"I want checks every ten minutes and can ye find some cool packs for me to place around the colonel, we need to get his temperature down." Carson order in full Doctor-Mode as the nurses near him treating John nodded as one of them, Shannon Best, went to retrieve the cool packs and helped Carson to place them strategically around John in places which the Scotsman knew would help bring the soldier's temperature down much quicker.

"Now, all we can do is wait I'm afraid."

"The Colonel's team is with Doctor Sheppard in the Delivery Suit and are waiting for some news."

"Aye, I'll go and see to them."

**--**

Teyla waited patiently as she comforted the stricken Leader in her time of grief at the prospect of losing her husband and friend, holding her close as she rubbed her arm reassuringly as Ronan gently placed the baby into the clear cot beside Elizabeth's bed in the quiet Delivery suit, as Rodney remained silent- not knowing what to say that would bring comfort to the diplomat.

As Ronan opened his mouth to speak, the doors swooshed open to reveal Carson who saw the scene and stopped abruptly as Elizabeth's sobs began to quieten as he drained herself. Teyla looked up with a sad face and nodded with a weak smile tugging the sides of her mouth as Carson came over slowly and came to stand beside Rodney as Elizabeth noticed the Scotsman for the first time through puffy eyes.

"Carson," Elizabeth mumbled, her voice thick from crying.

"How are ya lass?"

"I'm fine, how's John?"

Carson gave her a small wink and a weak smile. "He's doing as well as expected but he isn't out of the woods yet. The next day or so are the main concern; he contracted pneumonia- worse than before- but we've caught it early so hopefully the anti-biotics will kick in soon and we have re-stitched his lashes, which reopened when he hit them so they should be okay as long as we keep infection out of the wounds. Don't worry lass,he'll pull through- Now how are you really?"

Elizabeth nodded as she let out a deep, shaky breath she didn't realise she had been holding in and answered. "Tired, but it's John I'm concerned about- and the baby. People will be coming for her because of what she can do and I don't think we'll be able to stop them."

"They won't get to her, we won't let them." Ronan assured her roughly as Rodney looked up with hard eyes.

"She saved all of our lives today, nobody is going to hurt her, Elizabeth, and John sure as hell won't let anyone go near any of you."

"That's what scares me the most"

**--**

The machines mechanical- yet steady- beeps echoed out into the darkness of the Atlantis Infirmary, each monitor having a responsibility to both patient and Doctor to monitor pulse, blood pressure, heart rate, and temperature while the ventilator was entrusted to ensure the unmoving and pale man breathed after being pumped up- via and IV line which snaked along his bare left arm- with heavy sedation, anti-biotics, and morphine to name but a few of the medicines he had been placed upon to ensure his survival during the long night.

John Sheppard- Metaphorically speaking- was dead to the world as he lay in the infirmary bed under a whole spectrum of medication which would help him truly recover from the severity of his injuries which he had once again aggravated when he launched a rescue mission to save his wife, and then, unborn child from a female avatar who wanted their baby.

All the medical staff knew that John Sheppard was a true fighter but even they had to admit when they made their routine checks on the Lantean Military Leader, that Carson Beckett had performed yet another medical miracle for the soldier to have even made it out of surgery the first time, let alone a second.

The fever which had returned to his fragile body coursed through him like fire as the smell of Antiseptic hit the noses of any who came into this quiet section of the medical floor due to the constant changing of the unconscious mans badages and the white pad he lay ontop of which would prevent and leakage from his wounds onto the blanket which would lead to wet sheets and thus, spread infection even more which would enter the wounds, which were slowly repairing after being stitched up, and affect the man; giving his nervous system another jolt.

All indications so far, based on the regular checks of the on duty staff, was that John Sheppard's temperature had gone down slightly and there was no aggrivation of the surgical areas and his shoulder had been once again immobolised due to the collar bone lash he had sustained which had begun to bleed during surgery.

It was a long night indeed.


End file.
